Multiple sequence alignment - TraesCS3A01G158000

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Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS3A01G158000 chr3A 100.000 2236 0 0 2216 4451 155430389 155428154 0.000000e+00 4130
1 TraesCS3A01G158000 chr3A 100.000 1021 0 0 966 1986 155431639 155430619 0.000000e+00 1886
2 TraesCS3A01G158000 chr3A 100.000 647 0 0 1 647 155432604 155431958 0.000000e+00 1195
3 TraesCS3A01G158000 chr3A 93.137 102 6 1 3917 4018 215474134 215474234 9.970000e-32 148
4 TraesCS3A01G158000 chr3D 97.555 1554 35 3 2343 3896 137486734 137485184 0.000000e+00 2656
5 TraesCS3A01G158000 chr3D 95.682 579 14 2 1419 1986 137487597 137487019 0.000000e+00 920
6 TraesCS3A01G158000 chr3D 96.709 395 6 4 253 647 137488371 137487984 0.000000e+00 651
7 TraesCS3A01G158000 chr3D 90.575 435 16 6 4021 4451 137485170 137484757 1.810000e-153 553
8 TraesCS3A01G158000 chr3D 91.123 383 10 13 966 1335 137487963 137487592 8.600000e-137 497
9 TraesCS3A01G158000 chr3D 87.868 272 19 4 2 265 137490091 137489826 1.560000e-79 307
10 TraesCS3A01G158000 chr3D 98.425 127 2 0 2216 2342 137486981 137486855 1.610000e-54 224
11 TraesCS3A01G158000 chr3B 96.212 1584 53 2 2225 3806 200874529 200872951 0.000000e+00 2586
12 TraesCS3A01G158000 chr3B 91.602 1024 58 18 966 1986 200875567 200874569 0.000000e+00 1389
13 TraesCS3A01G158000 chr3B 91.718 652 26 12 2 647 200876217 200875588 0.000000e+00 880
14 TraesCS3A01G158000 chr3B 93.085 188 9 3 4267 4451 200864575 200864389 5.670000e-69 272
15 TraesCS3A01G158000 chr3B 94.898 98 5 0 3917 4014 509998903 509999000 2.140000e-33 154
16 TraesCS3A01G158000 chr7A 88.714 824 52 12 966 1766 527945349 527944544 0.000000e+00 968
17 TraesCS3A01G158000 chr7A 88.578 823 53 10 966 1766 312941754 312942557 0.000000e+00 961
18 TraesCS3A01G158000 chr7A 93.846 65 4 0 1130 1194 486142587 486142651 1.020000e-16 99
19 TraesCS3A01G158000 chr1D 87.186 398 51 0 2530 2927 165203043 165203440 1.890000e-123 453
20 TraesCS3A01G158000 chr1D 85.220 318 47 0 3089 3406 165203550 165203867 1.190000e-85 327
21 TraesCS3A01G158000 chr1B 87.186 398 51 0 2530 2927 246769232 246768835 1.890000e-123 453
22 TraesCS3A01G158000 chr1B 85.220 318 47 0 3089 3406 246768725 246768408 1.190000e-85 327
23 TraesCS3A01G158000 chr1A 85.220 318 47 0 3089 3406 216415546 216415229 1.190000e-85 327
24 TraesCS3A01G158000 chr1A 93.939 99 6 0 3917 4015 486680190 486680288 2.770000e-32 150
25 TraesCS3A01G158000 chr2A 79.560 318 63 2 3089 3405 77263699 77263383 4.480000e-55 226
26 TraesCS3A01G158000 chr7B 94.949 99 5 0 3917 4015 611967841 611967743 5.960000e-34 156
27 TraesCS3A01G158000 chr7B 95.385 65 3 0 1130 1194 453152880 453152816 2.190000e-18 104
28 TraesCS3A01G158000 chr5B 93.939 99 6 0 3917 4015 569225183 569225085 2.770000e-32 150
29 TraesCS3A01G158000 chr5A 93.939 99 6 0 3917 4015 53215071 53215169 2.770000e-32 150
30 TraesCS3A01G158000 chr5A 94.737 95 5 0 3917 4011 109342501 109342595 9.970000e-32 148
31 TraesCS3A01G158000 chr4B 94.792 96 5 0 3920 4015 27255752 27255657 2.770000e-32 150
32 TraesCS3A01G158000 chr2B 92.308 104 7 1 3917 4020 585193772 585193874 3.590000e-31 147
33 TraesCS3A01G158000 chr7D 95.385 65 3 0 1130 1194 436740207 436740143 2.190000e-18 104


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS3A01G158000 chr3A 155428154 155432604 4450 True 2403.666667 4130 100.000000 1 4451 3 chr3A.!!$R1 4450
1 TraesCS3A01G158000 chr3D 137484757 137490091 5334 True 829.714286 2656 93.991000 2 4451 7 chr3D.!!$R1 4449
2 TraesCS3A01G158000 chr3B 200872951 200876217 3266 True 1618.333333 2586 93.177333 2 3806 3 chr3B.!!$R2 3804
3 TraesCS3A01G158000 chr7A 527944544 527945349 805 True 968.000000 968 88.714000 966 1766 1 chr7A.!!$R1 800
4 TraesCS3A01G158000 chr7A 312941754 312942557 803 False 961.000000 961 88.578000 966 1766 1 chr7A.!!$F1 800
5 TraesCS3A01G158000 chr1D 165203043 165203867 824 False 390.000000 453 86.203000 2530 3406 2 chr1D.!!$F1 876
6 TraesCS3A01G158000 chr1B 246768408 246769232 824 True 390.000000 453 86.203000 2530 3406 2 chr1B.!!$R1 876

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
396 1876 0.680061 AATAGCACTAGCCGTAGCCC 59.320 55.000 0.00 0.0 43.56 5.19 F
397 1877 1.524863 ATAGCACTAGCCGTAGCCCG 61.525 60.000 0.00 0.0 43.56 6.13 F
1417 2924 2.092429 ACATATGCTGGGATTTCGGTGT 60.092 45.455 1.58 0.0 0.00 4.16 F
1664 3179 2.154462 AGGCAATCTCAAACCTCGTTG 58.846 47.619 0.00 0.0 0.00 4.10 F
3222 4886 2.612221 GCGGAACTACAGTTACAGCCTT 60.612 50.000 5.23 0.0 38.79 4.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1417 2924 0.245266 TTGATTACGGCAGAGCACGA 59.755 50.000 0.00 0.0 0.00 4.35 R
1644 3159 2.154462 CAACGAGGTTTGAGATTGCCT 58.846 47.619 0.00 0.0 0.00 4.75 R
2431 4074 0.037303 CATCCCTCCAACACACAGCT 59.963 55.000 0.00 0.0 0.00 4.24 R
3423 5087 1.185618 AGAGAACTGGTACGCAGGCA 61.186 55.000 13.68 0.0 0.00 4.75 R
4222 5888 0.179097 CCTAACCCTCGCTCTCAAGC 60.179 60.000 0.00 0.0 45.56 4.01 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
86 87 9.607333 ACCTAAGACAAATCTCATATATGGAGA 57.393 33.333 12.78 13.32 44.83 3.71
101 102 9.270640 CATATATGGAGAAAAGAGAAACAGAGG 57.729 37.037 4.68 0.00 0.00 3.69
139 140 7.027161 ACAAATCAAATGCAAAGTATCGGTAC 58.973 34.615 0.00 0.00 0.00 3.34
157 158 1.313812 ACCCCACACGATCTCGAGTC 61.314 60.000 13.13 8.49 40.95 3.36
238 251 5.359756 GCCAACAAATCTGAAACCTTTTCT 58.640 37.500 0.68 0.00 0.00 2.52
250 263 6.795399 TGAAACCTTTTCTTCAACTAGCAAG 58.205 36.000 0.00 0.00 0.00 4.01
395 1875 3.870633 ATAATAGCACTAGCCGTAGCC 57.129 47.619 0.00 0.00 43.56 3.93
396 1876 0.680061 AATAGCACTAGCCGTAGCCC 59.320 55.000 0.00 0.00 43.56 5.19
397 1877 1.524863 ATAGCACTAGCCGTAGCCCG 61.525 60.000 0.00 0.00 43.56 6.13
1210 2693 3.392882 CAGGTTTCTTGATTTTGCCCAC 58.607 45.455 0.00 0.00 0.00 4.61
1211 2694 2.368548 AGGTTTCTTGATTTTGCCCACC 59.631 45.455 0.00 0.00 0.00 4.61
1359 2864 3.882888 TGTCGAATTCTTGGGGATATTGC 59.117 43.478 3.52 0.00 0.00 3.56
1383 2890 5.527951 TGGTGTATTGTGCTTGTGAATTTC 58.472 37.500 0.00 0.00 0.00 2.17
1417 2924 2.092429 ACATATGCTGGGATTTCGGTGT 60.092 45.455 1.58 0.00 0.00 4.16
1566 3081 3.208594 TGCAGACAAGCATGCTATTAGG 58.791 45.455 23.00 12.13 42.98 2.69
1664 3179 2.154462 AGGCAATCTCAAACCTCGTTG 58.846 47.619 0.00 0.00 0.00 4.10
1733 3251 5.104151 TGTGGATATGTGATCAGCCCTTAAA 60.104 40.000 0.00 0.00 0.00 1.52
1911 3429 6.406370 TCCTACATTAATCCTATGCAATCGG 58.594 40.000 0.00 0.00 0.00 4.18
2249 3767 5.491982 AGTTGGTAGCAAATCTAACTCTGG 58.508 41.667 9.30 0.00 35.96 3.86
2341 3984 8.928448 TGATATCTTGATCCTTAAGCAAGTACT 58.072 33.333 16.24 0.00 39.85 2.73
2342 3985 9.202273 GATATCTTGATCCTTAAGCAAGTACTG 57.798 37.037 16.24 0.00 39.85 2.74
2343 3986 6.360370 TCTTGATCCTTAAGCAAGTACTGT 57.640 37.500 16.24 0.00 39.85 3.55
2344 3987 7.476540 TCTTGATCCTTAAGCAAGTACTGTA 57.523 36.000 16.24 0.00 39.85 2.74
2346 3989 6.599356 TGATCCTTAAGCAAGTACTGTACA 57.401 37.500 19.27 0.00 0.00 2.90
2347 3990 6.999950 TGATCCTTAAGCAAGTACTGTACAA 58.000 36.000 19.27 3.77 0.00 2.41
2348 3991 6.872020 TGATCCTTAAGCAAGTACTGTACAAC 59.128 38.462 19.27 8.42 0.00 3.32
2349 3992 6.164417 TCCTTAAGCAAGTACTGTACAACA 57.836 37.500 19.27 0.00 0.00 3.33
3222 4886 2.612221 GCGGAACTACAGTTACAGCCTT 60.612 50.000 5.23 0.00 38.79 4.35
3809 5475 0.546267 AGCTTCAGGCCTTCAGAGGA 60.546 55.000 0.00 0.00 46.74 3.71
3822 5488 6.777580 GGCCTTCAGAGGATTTATAATTTGGA 59.222 38.462 0.00 0.00 46.74 3.53
3826 5492 7.807977 TCAGAGGATTTATAATTTGGACTGC 57.192 36.000 0.00 0.00 0.00 4.40
3871 5537 4.153117 CAGTGTGGATTAGTCTTTGCACTC 59.847 45.833 8.08 5.41 34.25 3.51
3896 5562 3.196685 AGAGACTGGGACTGATGTTAAGC 59.803 47.826 0.00 0.00 0.00 3.09
3897 5563 2.093973 AGACTGGGACTGATGTTAAGCG 60.094 50.000 0.00 0.00 0.00 4.68
3899 5565 0.392461 TGGGACTGATGTTAAGCGCC 60.392 55.000 2.29 0.00 0.00 6.53
3900 5566 0.107654 GGGACTGATGTTAAGCGCCT 60.108 55.000 2.29 0.00 0.00 5.52
3901 5567 1.009829 GGACTGATGTTAAGCGCCTG 58.990 55.000 2.29 0.00 0.00 4.85
3903 5569 2.076863 GACTGATGTTAAGCGCCTGTT 58.923 47.619 2.29 0.00 0.00 3.16
3904 5570 2.076863 ACTGATGTTAAGCGCCTGTTC 58.923 47.619 2.29 0.00 0.00 3.18
3905 5571 2.076100 CTGATGTTAAGCGCCTGTTCA 58.924 47.619 2.29 0.00 0.00 3.18
3906 5572 2.076100 TGATGTTAAGCGCCTGTTCAG 58.924 47.619 2.29 0.00 0.00 3.02
3907 5573 0.804989 ATGTTAAGCGCCTGTTCAGC 59.195 50.000 2.29 0.00 0.00 4.26
3908 5574 1.234615 TGTTAAGCGCCTGTTCAGCC 61.235 55.000 2.29 0.00 0.00 4.85
3909 5575 2.032634 TTAAGCGCCTGTTCAGCCG 61.033 57.895 2.29 0.00 0.00 5.52
3913 5579 4.749310 CGCCTGTTCAGCCGCTCT 62.749 66.667 0.00 0.00 0.00 4.09
3914 5580 2.817396 GCCTGTTCAGCCGCTCTC 60.817 66.667 0.00 0.00 0.00 3.20
3915 5581 2.125350 CCTGTTCAGCCGCTCTCC 60.125 66.667 0.00 0.00 0.00 3.71
3916 5582 2.507992 CTGTTCAGCCGCTCTCCG 60.508 66.667 0.00 0.00 0.00 4.63
3917 5583 4.742201 TGTTCAGCCGCTCTCCGC 62.742 66.667 0.00 0.00 35.03 5.54
3936 5602 1.557651 CGGAGCGTCCTTTTAGTAGC 58.442 55.000 3.15 0.00 33.30 3.58
3937 5603 1.134560 CGGAGCGTCCTTTTAGTAGCT 59.865 52.381 0.00 0.00 37.69 3.32
3939 5605 3.786516 GAGCGTCCTTTTAGTAGCTCT 57.213 47.619 7.86 0.00 45.22 4.09
3940 5606 3.440228 GAGCGTCCTTTTAGTAGCTCTG 58.560 50.000 7.86 0.00 45.22 3.35
3941 5607 1.927838 GCGTCCTTTTAGTAGCTCTGC 59.072 52.381 0.00 0.00 0.00 4.26
3942 5608 2.674177 GCGTCCTTTTAGTAGCTCTGCA 60.674 50.000 0.00 0.00 0.00 4.41
3943 5609 3.182967 CGTCCTTTTAGTAGCTCTGCAG 58.817 50.000 7.63 7.63 0.00 4.41
3944 5610 3.119459 CGTCCTTTTAGTAGCTCTGCAGA 60.119 47.826 17.19 17.19 0.00 4.26
3945 5611 4.440802 CGTCCTTTTAGTAGCTCTGCAGAT 60.441 45.833 18.63 5.89 0.00 2.90
3946 5612 5.423886 GTCCTTTTAGTAGCTCTGCAGATT 58.576 41.667 18.63 11.37 0.00 2.40
3947 5613 6.574350 GTCCTTTTAGTAGCTCTGCAGATTA 58.426 40.000 18.63 10.31 0.00 1.75
3948 5614 7.213678 GTCCTTTTAGTAGCTCTGCAGATTAT 58.786 38.462 18.63 8.73 0.00 1.28
3949 5615 8.361139 GTCCTTTTAGTAGCTCTGCAGATTATA 58.639 37.037 18.63 7.69 0.00 0.98
3950 5616 8.361139 TCCTTTTAGTAGCTCTGCAGATTATAC 58.639 37.037 18.63 18.53 0.00 1.47
3951 5617 7.600752 CCTTTTAGTAGCTCTGCAGATTATACC 59.399 40.741 18.63 3.61 0.00 2.73
3952 5618 7.841282 TTTAGTAGCTCTGCAGATTATACCT 57.159 36.000 18.63 10.84 0.00 3.08
3953 5619 8.935614 TTTAGTAGCTCTGCAGATTATACCTA 57.064 34.615 18.63 9.89 0.00 3.08
3954 5620 8.568676 TTAGTAGCTCTGCAGATTATACCTAG 57.431 38.462 18.63 2.96 0.00 3.02
3955 5621 4.799564 AGCTCTGCAGATTATACCTAGC 57.200 45.455 18.63 13.54 0.00 3.42
3956 5622 4.155709 AGCTCTGCAGATTATACCTAGCA 58.844 43.478 18.63 0.00 0.00 3.49
3957 5623 4.590647 AGCTCTGCAGATTATACCTAGCAA 59.409 41.667 18.63 0.00 0.00 3.91
3958 5624 4.928615 GCTCTGCAGATTATACCTAGCAAG 59.071 45.833 18.63 0.90 0.00 4.01
3959 5625 4.887748 TCTGCAGATTATACCTAGCAAGC 58.112 43.478 13.74 0.00 0.00 4.01
3960 5626 3.999663 CTGCAGATTATACCTAGCAAGCC 59.000 47.826 8.42 0.00 0.00 4.35
3961 5627 3.390967 TGCAGATTATACCTAGCAAGCCA 59.609 43.478 0.00 0.00 0.00 4.75
3962 5628 3.748568 GCAGATTATACCTAGCAAGCCAC 59.251 47.826 0.00 0.00 0.00 5.01
3963 5629 4.503991 GCAGATTATACCTAGCAAGCCACT 60.504 45.833 0.00 0.00 0.00 4.00
3964 5630 5.233988 CAGATTATACCTAGCAAGCCACTC 58.766 45.833 0.00 0.00 0.00 3.51
3965 5631 4.284746 AGATTATACCTAGCAAGCCACTCC 59.715 45.833 0.00 0.00 0.00 3.85
3966 5632 0.753262 ATACCTAGCAAGCCACTCCG 59.247 55.000 0.00 0.00 0.00 4.63
3967 5633 1.956629 TACCTAGCAAGCCACTCCGC 61.957 60.000 0.00 0.00 0.00 5.54
3968 5634 2.581354 CTAGCAAGCCACTCCGCT 59.419 61.111 0.00 0.00 42.22 5.52
3969 5635 1.520342 CTAGCAAGCCACTCCGCTC 60.520 63.158 0.00 0.00 38.44 5.03
3970 5636 2.914777 CTAGCAAGCCACTCCGCTCC 62.915 65.000 0.00 0.00 38.44 4.70
4006 5672 2.572284 GGAGGGAGTCCGAACACG 59.428 66.667 2.26 0.00 34.84 4.49
4008 5674 3.644399 GAGGGAGTCCGAACACGGC 62.644 68.421 2.26 0.08 45.52 5.68
4009 5675 4.754667 GGGAGTCCGAACACGGCC 62.755 72.222 2.26 0.00 45.52 6.13
4010 5676 3.692406 GGAGTCCGAACACGGCCT 61.692 66.667 0.00 0.00 45.52 5.19
4011 5677 2.345760 GGAGTCCGAACACGGCCTA 61.346 63.158 0.00 0.00 45.52 3.93
4012 5678 1.588082 GAGTCCGAACACGGCCTAA 59.412 57.895 0.00 0.00 45.52 2.69
4013 5679 0.458025 GAGTCCGAACACGGCCTAAG 60.458 60.000 0.00 0.00 45.52 2.18
4014 5680 1.183676 AGTCCGAACACGGCCTAAGT 61.184 55.000 0.00 0.00 45.52 2.24
4015 5681 0.527565 GTCCGAACACGGCCTAAGTA 59.472 55.000 0.00 0.00 45.52 2.24
4016 5682 0.527565 TCCGAACACGGCCTAAGTAC 59.472 55.000 0.00 0.00 45.52 2.73
4017 5683 0.529378 CCGAACACGGCCTAAGTACT 59.471 55.000 0.00 0.00 40.29 2.73
4018 5684 1.468736 CCGAACACGGCCTAAGTACTC 60.469 57.143 0.00 0.00 40.29 2.59
4019 5685 1.200716 CGAACACGGCCTAAGTACTCA 59.799 52.381 0.00 0.00 0.00 3.41
4025 5691 3.031736 ACGGCCTAAGTACTCATGACAT 58.968 45.455 0.00 0.00 0.00 3.06
4101 5767 8.670521 TTGCTCCAGGATAATCTTATCTGATA 57.329 34.615 9.23 0.00 39.53 2.15
4132 5798 3.684788 ACTTGAGTGATGCGTTAATGTCC 59.315 43.478 0.00 0.00 0.00 4.02
4138 5804 3.060272 GTGATGCGTTAATGTCCTCATCG 60.060 47.826 0.00 0.00 34.64 3.84
4139 5805 2.951457 TGCGTTAATGTCCTCATCGA 57.049 45.000 0.00 0.00 32.56 3.59
4140 5806 2.809446 TGCGTTAATGTCCTCATCGAG 58.191 47.619 0.00 0.00 32.56 4.04
4141 5807 2.425668 TGCGTTAATGTCCTCATCGAGA 59.574 45.455 0.00 0.00 32.56 4.04
4142 5808 2.789893 GCGTTAATGTCCTCATCGAGAC 59.210 50.000 0.00 0.00 32.56 3.36
4143 5809 3.036633 CGTTAATGTCCTCATCGAGACG 58.963 50.000 0.00 0.00 32.56 4.18
4144 5810 3.487042 CGTTAATGTCCTCATCGAGACGT 60.487 47.826 0.00 0.00 32.56 4.34
4145 5811 4.421948 GTTAATGTCCTCATCGAGACGTT 58.578 43.478 12.79 12.79 32.56 3.99
4146 5812 5.575957 GTTAATGTCCTCATCGAGACGTTA 58.424 41.667 11.22 11.22 32.56 3.18
4147 5813 4.713824 AATGTCCTCATCGAGACGTTAA 57.286 40.909 7.90 0.00 32.56 2.01
4148 5814 4.920640 ATGTCCTCATCGAGACGTTAAT 57.079 40.909 0.00 0.00 0.00 1.40
4149 5815 4.028852 TGTCCTCATCGAGACGTTAATG 57.971 45.455 0.00 0.00 0.00 1.90
4150 5816 3.442625 TGTCCTCATCGAGACGTTAATGT 59.557 43.478 0.00 0.00 0.00 2.71
4151 5817 4.036352 GTCCTCATCGAGACGTTAATGTC 58.964 47.826 18.38 18.38 39.21 3.06
4152 5818 3.066342 TCCTCATCGAGACGTTAATGTCC 59.934 47.826 21.57 13.26 39.77 4.02
4153 5819 3.066900 CCTCATCGAGACGTTAATGTCCT 59.933 47.826 21.57 10.88 39.77 3.85
4154 5820 4.283678 CTCATCGAGACGTTAATGTCCTC 58.716 47.826 21.57 16.71 39.77 3.71
4155 5821 3.692593 TCATCGAGACGTTAATGTCCTCA 59.307 43.478 21.57 8.12 39.77 3.86
4156 5822 4.338400 TCATCGAGACGTTAATGTCCTCAT 59.662 41.667 21.57 9.85 39.77 2.90
4157 5823 4.288670 TCGAGACGTTAATGTCCTCATC 57.711 45.455 21.57 12.81 39.77 2.92
4158 5824 3.036633 CGAGACGTTAATGTCCTCATCG 58.963 50.000 21.57 19.27 39.77 3.84
4191 5857 2.290641 GTGTCTCAAACGGCAGATTTGT 59.709 45.455 10.03 0.00 38.08 2.83
4221 5887 1.279496 CAGACCAGAACCTCATGGGA 58.721 55.000 0.00 0.00 41.13 4.37
4222 5888 1.209019 CAGACCAGAACCTCATGGGAG 59.791 57.143 0.00 0.00 41.13 4.30
4262 5928 4.407296 AGGAGCTGACGGAGATATCTTTTT 59.593 41.667 6.70 0.00 0.00 1.94
4269 5935 5.105106 TGACGGAGATATCTTTTTGGCTACA 60.105 40.000 6.70 0.00 0.00 2.74
4270 5936 5.741011 ACGGAGATATCTTTTTGGCTACAA 58.259 37.500 6.70 0.00 34.07 2.41
4271 5937 5.585047 ACGGAGATATCTTTTTGGCTACAAC 59.415 40.000 6.70 0.00 36.06 3.32
4272 5938 5.817816 CGGAGATATCTTTTTGGCTACAACT 59.182 40.000 6.70 0.00 36.06 3.16
4273 5939 6.316390 CGGAGATATCTTTTTGGCTACAACTT 59.684 38.462 6.70 0.00 36.06 2.66
4287 5956 5.238583 GCTACAACTTAAGAGGCTCTTGAA 58.761 41.667 34.22 22.85 37.29 2.69
4308 5977 8.921353 TTGAAGAAAGTCTAGTACTCTACAGT 57.079 34.615 0.00 0.00 37.50 3.55
4355 6024 9.014297 ACTTCAAATAAAAATGAGAACGGAGAT 57.986 29.630 0.00 0.00 0.00 2.75
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
75 76 9.270640 CCTCTGTTTCTCTTTTCTCCATATATG 57.729 37.037 5.68 5.68 0.00 1.78
81 82 3.973973 TCCCTCTGTTTCTCTTTTCTCCA 59.026 43.478 0.00 0.00 0.00 3.86
86 87 5.373812 TCAAGTCCCTCTGTTTCTCTTTT 57.626 39.130 0.00 0.00 0.00 2.27
90 91 6.287589 TCTTATCAAGTCCCTCTGTTTCTC 57.712 41.667 0.00 0.00 0.00 2.87
101 102 7.814107 TGCATTTGATTTGTTCTTATCAAGTCC 59.186 33.333 0.00 0.00 40.65 3.85
139 140 1.433879 GACTCGAGATCGTGTGGGG 59.566 63.158 21.68 0.00 44.60 4.96
157 158 2.036733 TCTAGTGGGTGTGAGTTTTCCG 59.963 50.000 0.00 0.00 0.00 4.30
189 195 1.041437 GACGGAGGTGAGGATTAGGG 58.959 60.000 0.00 0.00 0.00 3.53
197 210 2.179517 GCAGTCGACGGAGGTGAG 59.820 66.667 20.25 0.51 0.00 3.51
238 251 2.806244 GGTTCGAAGCTTGCTAGTTGAA 59.194 45.455 19.71 0.00 0.00 2.69
250 263 2.096013 GCCACTATCTTTGGTTCGAAGC 59.904 50.000 20.13 20.13 36.40 3.86
398 1878 2.873557 TTAGGGAGGACGGAGGCAGG 62.874 65.000 0.00 0.00 0.00 4.85
439 1919 2.390599 GCAATGAAGCGGCTCGACA 61.391 57.895 1.45 4.94 0.00 4.35
1274 2778 5.544176 AGATCCCTATTCGAAGCCAAGAATA 59.456 40.000 3.35 5.59 38.04 1.75
1283 2787 4.130118 CAAACCCAGATCCCTATTCGAAG 58.870 47.826 3.35 0.00 0.00 3.79
1291 2795 1.466858 TTTCCCAAACCCAGATCCCT 58.533 50.000 0.00 0.00 0.00 4.20
1359 2864 4.771590 ATTCACAAGCACAATACACCAG 57.228 40.909 0.00 0.00 0.00 4.00
1383 2890 2.615447 AGCATATGTGAAATGGCAGACG 59.385 45.455 4.29 0.00 0.00 4.18
1417 2924 0.245266 TTGATTACGGCAGAGCACGA 59.755 50.000 0.00 0.00 0.00 4.35
1566 3081 6.645003 CCCAATTTTTACAAGGTAGAAACTGC 59.355 38.462 0.00 0.00 0.00 4.40
1644 3159 2.154462 CAACGAGGTTTGAGATTGCCT 58.846 47.619 0.00 0.00 0.00 4.75
1664 3179 9.719355 AATAAAATGGGACCAGAAAACAAATAC 57.281 29.630 0.00 0.00 0.00 1.89
1733 3251 6.498651 CCTGTACTCCACTTTATATCCTCCAT 59.501 42.308 0.00 0.00 0.00 3.41
1795 3313 7.835682 TCATCCAATGAAAGACCAAGATGTTAT 59.164 33.333 0.00 0.00 36.11 1.89
1911 3429 5.643379 TCCACCAAATGAAATAAGCAGTC 57.357 39.130 0.00 0.00 0.00 3.51
2341 3984 6.931840 TGCTTACATGTATTCACTGTTGTACA 59.068 34.615 6.36 0.00 0.00 2.90
2342 3985 7.359262 TGCTTACATGTATTCACTGTTGTAC 57.641 36.000 6.36 0.00 0.00 2.90
2343 3986 7.971183 TTGCTTACATGTATTCACTGTTGTA 57.029 32.000 6.36 0.00 0.00 2.41
2344 3987 6.875948 TTGCTTACATGTATTCACTGTTGT 57.124 33.333 6.36 0.00 0.00 3.32
2346 3989 7.814107 CCAAATTGCTTACATGTATTCACTGTT 59.186 33.333 6.36 1.31 0.00 3.16
2347 3990 7.315142 CCAAATTGCTTACATGTATTCACTGT 58.685 34.615 6.36 0.00 0.00 3.55
2348 3991 6.753279 CCCAAATTGCTTACATGTATTCACTG 59.247 38.462 6.36 5.47 0.00 3.66
2349 3992 6.663093 TCCCAAATTGCTTACATGTATTCACT 59.337 34.615 6.36 0.00 0.00 3.41
2350 3993 6.862209 TCCCAAATTGCTTACATGTATTCAC 58.138 36.000 6.36 0.00 0.00 3.18
2357 4000 5.327616 TGTGATCCCAAATTGCTTACATG 57.672 39.130 0.00 0.00 0.00 3.21
2429 4072 1.656587 TCCCTCCAACACACAGCTAT 58.343 50.000 0.00 0.00 0.00 2.97
2431 4074 0.037303 CATCCCTCCAACACACAGCT 59.963 55.000 0.00 0.00 0.00 4.24
3222 4886 4.776322 CCATTGGCGCCGACCTCA 62.776 66.667 21.40 0.00 0.00 3.86
3279 4943 3.637273 ACCTTCCGGTGGCTGTCC 61.637 66.667 14.48 0.00 43.51 4.02
3423 5087 1.185618 AGAGAACTGGTACGCAGGCA 61.186 55.000 13.68 0.00 0.00 4.75
3809 5475 4.215109 AGGCCGCAGTCCAAATTATAAAT 58.785 39.130 0.00 0.00 0.00 1.40
3822 5488 1.704641 TCATCATACTAGGCCGCAGT 58.295 50.000 16.10 16.10 0.00 4.40
3826 5492 3.429547 GCTGGTATCATCATACTAGGCCG 60.430 52.174 2.41 0.00 41.99 6.13
3871 5537 0.743688 CATCAGTCCCAGTCTCTCCG 59.256 60.000 0.00 0.00 0.00 4.63
3878 5544 1.676014 GCGCTTAACATCAGTCCCAGT 60.676 52.381 0.00 0.00 0.00 4.00
3882 5548 1.009829 CAGGCGCTTAACATCAGTCC 58.990 55.000 7.64 0.00 0.00 3.85
3899 5565 2.507992 CGGAGAGCGGCTGAACAG 60.508 66.667 7.50 0.00 0.00 3.16
3900 5566 4.742201 GCGGAGAGCGGCTGAACA 62.742 66.667 7.50 0.00 37.38 3.18
3916 5582 1.557651 CTACTAAAAGGACGCTCCGC 58.442 55.000 0.00 0.00 42.75 5.54
3917 5583 1.134560 AGCTACTAAAAGGACGCTCCG 59.865 52.381 0.00 0.00 42.75 4.63
3918 5584 2.427812 AGAGCTACTAAAAGGACGCTCC 59.572 50.000 0.00 0.00 43.51 4.70
3919 5585 3.440228 CAGAGCTACTAAAAGGACGCTC 58.560 50.000 0.00 0.00 42.98 5.03
3920 5586 2.417515 GCAGAGCTACTAAAAGGACGCT 60.418 50.000 0.00 0.00 0.00 5.07
3921 5587 1.927838 GCAGAGCTACTAAAAGGACGC 59.072 52.381 0.00 0.00 0.00 5.19
3922 5588 3.119459 TCTGCAGAGCTACTAAAAGGACG 60.119 47.826 13.74 0.00 0.00 4.79
3923 5589 4.457834 TCTGCAGAGCTACTAAAAGGAC 57.542 45.455 13.74 0.00 0.00 3.85
3924 5590 5.683876 AATCTGCAGAGCTACTAAAAGGA 57.316 39.130 22.96 0.00 0.00 3.36
3925 5591 7.600752 GGTATAATCTGCAGAGCTACTAAAAGG 59.399 40.741 22.96 0.00 0.00 3.11
3926 5592 8.364142 AGGTATAATCTGCAGAGCTACTAAAAG 58.636 37.037 22.96 0.00 0.00 2.27
3927 5593 8.251383 AGGTATAATCTGCAGAGCTACTAAAA 57.749 34.615 22.96 0.00 0.00 1.52
3928 5594 7.841282 AGGTATAATCTGCAGAGCTACTAAA 57.159 36.000 22.96 0.00 0.00 1.85
3929 5595 7.121463 GCTAGGTATAATCTGCAGAGCTACTAA 59.879 40.741 22.96 12.70 0.00 2.24
3930 5596 6.600032 GCTAGGTATAATCTGCAGAGCTACTA 59.400 42.308 22.96 16.31 0.00 1.82
3931 5597 5.417580 GCTAGGTATAATCTGCAGAGCTACT 59.582 44.000 22.96 16.07 0.00 2.57
3932 5598 5.184096 TGCTAGGTATAATCTGCAGAGCTAC 59.816 44.000 22.96 19.99 0.00 3.58
3933 5599 5.325239 TGCTAGGTATAATCTGCAGAGCTA 58.675 41.667 22.96 15.71 0.00 3.32
3934 5600 4.155709 TGCTAGGTATAATCTGCAGAGCT 58.844 43.478 22.96 15.11 0.00 4.09
3935 5601 4.527509 TGCTAGGTATAATCTGCAGAGC 57.472 45.455 22.96 16.14 0.00 4.09
3936 5602 4.928615 GCTTGCTAGGTATAATCTGCAGAG 59.071 45.833 22.96 6.01 0.00 3.35
3937 5603 4.262635 GGCTTGCTAGGTATAATCTGCAGA 60.263 45.833 20.79 20.79 0.00 4.26
3938 5604 3.999663 GGCTTGCTAGGTATAATCTGCAG 59.000 47.826 7.63 7.63 0.00 4.41
3939 5605 3.390967 TGGCTTGCTAGGTATAATCTGCA 59.609 43.478 0.00 0.00 0.00 4.41
3940 5606 3.748568 GTGGCTTGCTAGGTATAATCTGC 59.251 47.826 0.00 0.00 0.00 4.26
3941 5607 5.220710 AGTGGCTTGCTAGGTATAATCTG 57.779 43.478 0.00 0.00 0.00 2.90
3942 5608 4.284746 GGAGTGGCTTGCTAGGTATAATCT 59.715 45.833 0.00 0.00 0.00 2.40
3943 5609 4.570930 GGAGTGGCTTGCTAGGTATAATC 58.429 47.826 0.00 0.00 0.00 1.75
3944 5610 3.006967 CGGAGTGGCTTGCTAGGTATAAT 59.993 47.826 0.00 0.00 0.00 1.28
3945 5611 2.364324 CGGAGTGGCTTGCTAGGTATAA 59.636 50.000 0.00 0.00 0.00 0.98
3946 5612 1.961394 CGGAGTGGCTTGCTAGGTATA 59.039 52.381 0.00 0.00 0.00 1.47
3947 5613 0.753262 CGGAGTGGCTTGCTAGGTAT 59.247 55.000 0.00 0.00 0.00 2.73
3948 5614 1.956629 GCGGAGTGGCTTGCTAGGTA 61.957 60.000 0.00 0.00 0.00 3.08
3949 5615 2.982130 CGGAGTGGCTTGCTAGGT 59.018 61.111 0.00 0.00 0.00 3.08
3950 5616 2.512515 GCGGAGTGGCTTGCTAGG 60.513 66.667 0.00 0.00 0.00 3.02
3951 5617 1.520342 GAGCGGAGTGGCTTGCTAG 60.520 63.158 0.00 0.00 44.93 3.42
3952 5618 2.579201 GAGCGGAGTGGCTTGCTA 59.421 61.111 0.00 0.00 44.93 3.49
3953 5619 4.400961 GGAGCGGAGTGGCTTGCT 62.401 66.667 0.00 0.00 44.93 3.91
3989 5655 2.572284 CGTGTTCGGACTCCCTCC 59.428 66.667 0.00 0.00 35.33 4.30
3999 5665 1.200716 TGAGTACTTAGGCCGTGTTCG 59.799 52.381 0.00 0.00 0.00 3.95
4000 5666 3.119245 TCATGAGTACTTAGGCCGTGTTC 60.119 47.826 0.00 0.00 0.00 3.18
4001 5667 2.829720 TCATGAGTACTTAGGCCGTGTT 59.170 45.455 0.00 0.00 0.00 3.32
4002 5668 2.165845 GTCATGAGTACTTAGGCCGTGT 59.834 50.000 0.00 0.00 0.00 4.49
4003 5669 2.165641 TGTCATGAGTACTTAGGCCGTG 59.834 50.000 0.00 0.00 0.00 4.94
4004 5670 2.453521 TGTCATGAGTACTTAGGCCGT 58.546 47.619 0.00 0.00 0.00 5.68
4005 5671 3.319405 AGATGTCATGAGTACTTAGGCCG 59.681 47.826 0.00 0.00 0.00 6.13
4006 5672 4.946478 AGATGTCATGAGTACTTAGGCC 57.054 45.455 0.00 0.00 0.00 5.19
4007 5673 5.751028 GTCAAGATGTCATGAGTACTTAGGC 59.249 44.000 0.00 0.00 0.00 3.93
4008 5674 6.276847 GGTCAAGATGTCATGAGTACTTAGG 58.723 44.000 0.00 0.00 0.00 2.69
4009 5675 6.276847 GGGTCAAGATGTCATGAGTACTTAG 58.723 44.000 0.00 0.00 0.00 2.18
4010 5676 5.128827 GGGGTCAAGATGTCATGAGTACTTA 59.871 44.000 0.00 0.00 0.00 2.24
4011 5677 4.080863 GGGGTCAAGATGTCATGAGTACTT 60.081 45.833 0.00 0.00 0.00 2.24
4012 5678 3.452627 GGGGTCAAGATGTCATGAGTACT 59.547 47.826 0.00 0.00 0.00 2.73
4013 5679 3.738281 CGGGGTCAAGATGTCATGAGTAC 60.738 52.174 0.00 0.00 0.00 2.73
4014 5680 2.430694 CGGGGTCAAGATGTCATGAGTA 59.569 50.000 0.00 0.00 0.00 2.59
4015 5681 1.208052 CGGGGTCAAGATGTCATGAGT 59.792 52.381 0.00 0.00 0.00 3.41
4016 5682 1.473965 CCGGGGTCAAGATGTCATGAG 60.474 57.143 0.00 0.00 0.00 2.90
4017 5683 0.541392 CCGGGGTCAAGATGTCATGA 59.459 55.000 0.00 0.00 0.00 3.07
4018 5684 1.097547 GCCGGGGTCAAGATGTCATG 61.098 60.000 2.18 0.00 0.00 3.07
4019 5685 1.224592 GCCGGGGTCAAGATGTCAT 59.775 57.895 2.18 0.00 0.00 3.06
4025 5691 1.531739 GCAAAATGCCGGGGTCAAGA 61.532 55.000 2.18 0.00 37.42 3.02
4067 5733 5.708736 TTATCCTGGAGCAAAAGTCCATA 57.291 39.130 1.52 0.00 43.33 2.74
4076 5742 7.565190 ATCAGATAAGATTATCCTGGAGCAA 57.435 36.000 1.52 0.00 40.26 3.91
4101 5767 4.081972 ACGCATCACTCAAGTCACTAATCT 60.082 41.667 0.00 0.00 0.00 2.40
4118 5784 3.381045 TCGATGAGGACATTAACGCATC 58.619 45.455 0.00 0.00 36.82 3.91
4132 5798 4.201920 TGAGGACATTAACGTCTCGATGAG 60.202 45.833 1.22 0.00 36.12 2.90
4138 5804 4.035324 TCTCGATGAGGACATTAACGTCTC 59.965 45.833 1.22 0.00 36.82 3.36
4139 5805 3.945921 TCTCGATGAGGACATTAACGTCT 59.054 43.478 1.22 0.00 36.82 4.18
4140 5806 4.036352 GTCTCGATGAGGACATTAACGTC 58.964 47.826 0.00 0.00 36.82 4.34
4141 5807 3.487042 CGTCTCGATGAGGACATTAACGT 60.487 47.826 3.78 0.00 36.82 3.99
4142 5808 3.036633 CGTCTCGATGAGGACATTAACG 58.963 50.000 3.78 0.00 36.82 3.18
4143 5809 3.372954 CCGTCTCGATGAGGACATTAAC 58.627 50.000 3.78 0.00 36.82 2.01
4144 5810 2.361119 CCCGTCTCGATGAGGACATTAA 59.639 50.000 3.78 0.00 36.82 1.40
4145 5811 1.954382 CCCGTCTCGATGAGGACATTA 59.046 52.381 3.78 0.00 36.82 1.90
4146 5812 0.747255 CCCGTCTCGATGAGGACATT 59.253 55.000 3.78 0.00 36.82 2.71
4147 5813 1.739338 GCCCGTCTCGATGAGGACAT 61.739 60.000 3.78 0.00 39.67 3.06
4148 5814 2.415608 GCCCGTCTCGATGAGGACA 61.416 63.158 3.78 0.00 32.72 4.02
4149 5815 1.945354 TTGCCCGTCTCGATGAGGAC 61.945 60.000 2.26 0.00 32.72 3.85
4150 5816 1.680989 TTGCCCGTCTCGATGAGGA 60.681 57.895 2.26 0.00 32.72 3.71
4151 5817 1.519455 GTTGCCCGTCTCGATGAGG 60.519 63.158 0.00 0.00 0.00 3.86
4152 5818 1.874019 CGTTGCCCGTCTCGATGAG 60.874 63.158 0.00 0.00 0.00 2.90
4153 5819 2.180769 CGTTGCCCGTCTCGATGA 59.819 61.111 0.00 0.00 0.00 2.92
4221 5887 0.820871 CTAACCCTCGCTCTCAAGCT 59.179 55.000 0.00 0.00 46.91 3.74
4222 5888 0.179097 CCTAACCCTCGCTCTCAAGC 60.179 60.000 0.00 0.00 45.56 4.01
4262 5928 3.173965 AGAGCCTCTTAAGTTGTAGCCA 58.826 45.455 1.63 0.00 0.00 4.75
4269 5935 6.596621 ACTTTCTTCAAGAGCCTCTTAAGTT 58.403 36.000 6.66 0.00 33.78 2.66
4270 5936 6.042666 AGACTTTCTTCAAGAGCCTCTTAAGT 59.957 38.462 15.88 15.88 34.69 2.24
4271 5937 6.463360 AGACTTTCTTCAAGAGCCTCTTAAG 58.537 40.000 6.66 9.24 33.78 1.85
4272 5938 6.426646 AGACTTTCTTCAAGAGCCTCTTAA 57.573 37.500 6.66 0.00 33.78 1.85
4273 5939 6.722129 ACTAGACTTTCTTCAAGAGCCTCTTA 59.278 38.462 6.66 0.00 33.78 2.10
4287 5956 9.218440 GTGTTACTGTAGAGTACTAGACTTTCT 57.782 37.037 0.00 0.00 39.06 2.52
4328 5997 8.504005 TCTCCGTTCTCATTTTTATTTGAAGTC 58.496 33.333 0.00 0.00 0.00 3.01
4348 6017 6.040878 CGGTCTTTAAAAGTATGATCTCCGT 58.959 40.000 0.00 0.00 0.00 4.69
4355 6024 5.246656 TCCAGTCCGGTCTTTAAAAGTATGA 59.753 40.000 0.00 0.00 35.57 2.15


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.